publication . Doctoral thesis . 2010

The annotation of transposable elements through the understanding of their diversification

Flutre, Timothée;
Open Access French
  • Published: 28 Oct 2010
  • Publisher: HAL CCSD
  • Country: France
mention "très honorable avec félicitations"; Any living organism is the result of complex interactions between its genome and its environment, interactions characterizedby transfers of matter and energy required for the survival of the organism and the transmission of its genome. Since the discovery in the years 1910 that the chromosome is the mechanical basis of the genetic information, the biologists study genomes in order to decipher the mecanisms and processes operating in the development of organisms and the evolution of populations. Thanks to the technological improvements of the last decades, several genomes were fully sequenced, their number increasing q...
free text keywords: annotation, génomique, bioinformatique, élément transposable, variation structurale, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, genomics, bioinformatics, transposable element, structural variation
84 references, page 1 of 6

a annexes 179 a.1 Article "Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita" 179 a.2 Article "Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements" 193 1 1 0 2 n a J 7 2 - 1 n o i s r e v , 2 4 2 0 6 5 0 0 - l e t 1 1 0 2 n a J 7 2 - 1 n o i s r e v , 2 4 2 0 6 5 0 0 - l e t p u o r 1. Trudgill, D.L. & Blok, V.C. Apomictic, polyphagous root-knot nematodes: exceptionally G successful and damaging biotrophic root pathogens. Annu. Rev. Phytopathol. 39, ng 53-77 (2001).

ih2. Blaxter, M.L. Nematoda: genes, genomes and the evolution of parasitism. Adv. is Parasitol. 54, 101-195 (2003). [OpenAIRE]

lb3. Caillaud, M.C. et al. MAP65-3 Microtubule-associated protein is essential for nemau tode-induced giant cell ontogenesis in Arabidopsis. Plant Cell 20, 423-437 P (2008). [OpenAIRE]

re4. Caillaud, M.C. et al. Root-knot nematodes manipulate plant cell functions during a tu compatible interaction. J. Plant Physiol. 165, 104-113 (2008). a5. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: N a platform for investigating biology. Science 282, 2012-2018 (1998). 086. Stein, L.D. et al. The genome sequence of Caenorhabditis briggsae: a platform for 0 comparative genomics. PLoS Biol. 1, E45 (2003).

27. Ghedin, E. et al. Draft genome of the filarial nematode parasite Brugia malayi. Science © 317, 1756-1760 (2007).

8. Jaffe, D.B. et al. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 13, 91-96 (2003).

9. Leroy, S., Duperray, C. & Morand, S. Flow cytometry for parasite nematode genome size measurement. Mol. Biochem. Parasitol. 128, 91-93 (2003).

10. Triantaphyllou, A.C. in An Advance Treatise on Meloidogyne vol. 1 (eds. Sasser, J.N. & Carter, C.C.) 113-126, (North Carolina State University Graphics, Raleigh, USA, 1985).

11. Castagnone-Sereno, P. Genetic variability and adaptive evolution in parthenogenetic root-knot nematodes. Heredity 96, 282-289 (2006). [OpenAIRE]

12. Mark Welch, D.B., Cummings, M.P., Hillis, D.M. & Meselson, M. Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families. Proc. Natl. Acad. Sci. USA 101, 1622-1625 (2004).

13. Piotte, C., Castagnone-Sereno, P., Bongiovanni, M., Dalmasso, A. & Abad, P. Cloning and characterization of two satellite DNAs in the low-C-value genome of the nematode Meloidogyne spp. Gene 138, 175-180 (1994). [OpenAIRE]

14. Foissac, S. & Schiex, T. Integrating alternative splicing detection into gene prediction. BMC Bioinformatics 6, 25 (2005). [OpenAIRE]

15. Li, L., Stoeckert, C.J. Jr. & Roos, D.S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003). [OpenAIRE]

16. Davis, E.L., Hussey, R.S. & Baum, T.J. Getting to the roots of parasitism by nematodes. Trends Parasitol. 20, 134-141 (2004).

17. Wei, Y.D. et al. Molecular cloning, expression, and enzymatic activity of a novel endogenous cellulase from the mulberry longicorn beetle, Apriona germari. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 145, 220-229 (2006).

84 references, page 1 of 6
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